Thermodynamic studies of transfer ribonucleic acids. I. Magnesium binding to yeast phenylalanine transfer ribonucleic acid

Rialdi, G.; Levy, Julia G.; Biltonen, Rodney L.

doi:10.1021/bi00763a014

Cited by 95 publications

(79 citation statements)

References 20 publications

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“…⌬G N-Mg2ϩ and ⌬G I-Mg2ϩ can only be obtained by measuring the extent of Mg 2ϩ interaction with an RNA, for instance by equilibrium dialysis. These kinds of measurements have been done for only a few folded tRNAs (2,(7)(8)(9) and one rRNA fragment (10). Thus, for most RNAs, we do not know the overall contribution of Mg 2ϩ to RNA folding (⌬⌬G Mg2ϩ ) or the degree to which Mg 2ϩ affects the free energies of folded and partially folded forms.…”

Section: [1]mentioning

confidence: 99%

Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Grilley

Soto²,

Draper³

2006

Proc. Natl. Acad. Sci. U.S.A.

124

184

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Mg 2؉ ions are very effective at stabilizing tertiary structures in RNAs. In most cases, folding of an RNA is so strongly coupled to its interactions with Mg 2؉ that it is difficult to separate free energies of Mg 2؉ -RNA interactions from the intrinsic free energy of RNA folding. To devise quantitative models accounting for this phenomenon of Mg 2؉ -induced RNA folding, it is necessary to independently determine Mg 2؉ -RNA interaction free energies for folded and unfolded RNA forms. In this work, the energetics of Mg 2؉ -RNA interactions are derived from an assay that measures the effective concentration of Mg 2؉ in the presence of RNA. These measurements are used with other measures of RNA stability to develop an overall picture of the energetics of Mg 2؉ -induced RNA folding. Two different RNAs are discussed, a pseudoknot and an rRNA fragment. Both RNAs interact strongly with Mg 2؉ when partially unfolded, but the two folded RNAs differ dramatically in their inherent stability in the absence of Mg 2؉ and in the free energy of their interactions with Mg 2؉ . From these results, it appears that any comprehensive framework for understanding Mg 2؉ -induced stabilization of RNA will have to (i) take into account the interactions of ions with the partially unfolded RNAs and (ii) identify factors responsible for the widely different strengths with which folded tertiary structures interact with Mg 2؉ .cations ͉ ion interaction coefficients ͉ Wyman linkage relations M g 2ϩ ions strongly stabilize RNA tertiary structures under conditions that only weakly affect RNA secondary structure stability, a phenomenon first studied in the folding of transfer RNA (1, 2). Although the sensitivity of RNA folding to Mg 2ϩ has been amply documented for many RNAs, it is still unknown how this sensitivity is quantitatively related to the strengths of Mg 2ϩ -RNA interactions. Thus, for most RNAs, the magnitude of the intrinsic RNA instability is unknown, nor is it known how much more favorably Mg 2ϩ interacts with the native RNA structure than with structures from which folding takes place. Lacking this fundamental overview of Mg 2ϩ -RNA interaction free energies, it has not been possible to carry out extensive evaluations of theoretical models that seek to explain Mg 2ϩ -induced RNA folding in terms of the underlying physical interactions (3, 4).In this article, we parse the tertiary folding of two different RNAs into the intrinsic free energy of folding in the absence of Mg 2ϩ and the free energies of Mg 2ϩ interactions with folded and partially folded states. To obtain the relevant free energies, we devised a practical experimental method for measuring the effect of RNA on Mg 2ϩ ion activities and derived the equations necessary for extracting Mg 2ϩ -RNA interaction free energies from the experimental data. The two RNAs have vastly different stabilities in the absence of Mg 2ϩ and correspondingly large differences in the favorable interactions of the native RNA structures with Mg 2ϩ . Clearly, different RNAs use different strategies ...

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Section: [1]mentioning

confidence: 99%

Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Grilley

Soto²,

Draper³

2006

Proc. Natl. Acad. Sci. U.S.A.

124

184

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“…Mg 2þ ion binding to yeast tRNA Phe data was taken from Rialdi et al (1972), who measured ion binding calorimetrically, and from Rö mer & Hach (1975), who used the fluorescence indicator 8-hydroxylquinoline 5-sulfonic acid (HQS) to monitor Mg 2þ association.…”

Section: Ion Binding Measurementsmentioning

confidence: 99%

“…This approach neglects small, but measurable, differences between the mutant and wild-type P4P6 solution structures in high-salt concen- . Data in 10 mM Na þ background (left, triangles) are taken from Rialdi et al (1972), data in 32 mM Na þ background (right, squares) are from Rö mer & Hach (1975). Theoretical predictions were obtained from PB calculations using the PDB coordinates (thin, solid lines) or the reconstructed bead model with uniformly assigned charges (thick, dashed lines).…”

Section: Ion Binding Pb Calculationsmentioning

confidence: 99%

Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling

et al. 2007

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Several algorithms are available to reconstruct low‐resolution electron density maps of biological macromolecules from small‐angle solution scattering data. These algorithms have been extensively applied to proteins and protein complexes. Here, we demonstrate their applicability to nucleic acids by reconstructing a set of RNA and DNA molecules of known three‐dimensional structure from their small‐angle X‐ray scattering profiles. The overall size and shape of the molecules get reproduced well in all tested cases. Furthermore, we show that the generated bead models can be used as inputs for electrostatic calculations. The number of ions bound under different solution conditions computed from numerical solutions of the Poisson–Boltzmann equation for bead models agrees very well with results of calculations on all atom models derived from crystallography. The predictions from Poisson–Boltzmann theory also agree generally well with experimentally determined ion binding numbers.

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“…The first key issue in the ion electrostatics is how diffuse ions are distributed around the RNA molecule [9][10][11][12][13][14][15][16][17][18][19]. There have been several useful experimental methods developed for the quantification of the ion atmosphere around nucleic acids.…”

Section: Distribution Of the Bound Ionsmentioning

confidence: 99%

“…There have been several useful experimental methods developed for the quantification of the ion atmosphere around nucleic acids. The methods include small angle X-ray scattering (SAXS) [9][10][11][12], the ion-counting method [13], and the thermodynamic method [14][15][16][17][18][19]. These methods have been successfully used to quantify the ion distribution, the competition between the different species of the ions, and the folding thermodynamics [16,17]; see Table 1.…”

Section: Distribution Of the Bound Ionsmentioning

confidence: 99%

3 Importance of Diffuse Metal Ion Binding to RNA

Tan¹,

Chen²

2015

Structural and Catalytic Roles of Metal Ions in RNA

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RNAs are highly charged polyanionic molecules. RNA structure and function are strongly correlated with the ionic condition of the solution. The primary focus of this article is on the role of diffusive ions in RNA folding. Due to the long-range nature of electrostatic interactions, the diffuse ions can contribute significantly to RNA structural stability and folding kinetics. We present an overview of the experimental findings as well as the theoretical developments on the diffuse ion effects in RNA folding. This review places heavy emphasis on the effect of magnesium ions. Magnesium ions play a highly efficient role in stabilizing RNA tertiary structures and promoting tertiary structural folding. The highly efficient role goes beyond the mean-field effect such as the ionic strength. In addition to the effects of specific ion binding and ion dehydration, ion-ion correlation for the diffuse ions can contribute to the efficient role of the multivalent ions such as the magnesium ions in RNA folding.

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Thermodynamic studies of transfer ribonucleic acids. I. Magnesium binding to yeast phenylalanine transfer ribonucleic acid

Cited by 95 publications

References 20 publications

Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling

3 Importance of Diffuse Metal Ion Binding to RNA

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Thermodynamic studies of transfer ribonucleic acids. I. Magnesium binding to yeast phenylalanine transfer ribonucleic acid

Cited by 95 publications

References 20 publications

Mg 2+ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Mg 2+ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling

3 Importance of Diffuse Metal Ion Binding to RNA

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Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures